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Java
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Source code in github,
built with datadrivencv package

Last updated in Sep, 2022

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Woei-Yuh Saw

I am currently a postdoctoral researcher at Baker Heart and Diabetes Institute in the System Genomics lab.

I have a strong interest in infer links with human complext traits by leveraging integrative multi-omics approaches into clinical environments to enable optimal data-supported decision making.

My academic research primarily explores genetic variation across global populations using multi-omics approaches and integrative omics for health and diseases.

Education

P.h.D

Saw Swee Hock School of Public Health
National University of Singapore

Singapore, SG

2019 - 2013

  • Under supervison of Prof Yik-Ying Teo, Biostatistic and Modelling Domain
  • Thesis title:“Mapping the natural variation of global populations”

B.Comp.

School of Computing
National University of Singapore

Singapore, SG

2011 - 2007

  • Major in Computational Biology

Research Experience

Honorary Fellow

Baker Department of Cardiometabolic Health
University of Melbourne

Melbourne, AU

Today - 2021

  • Collaborated with Dr Shu Mei Teo
  • Explored polygenic risk prediction on cardiometabolic diseases and its related traits in non-European populations
  • Performed polygenic risk scores calculation and compilation for cardiometabolic diseases, immune diseases, diseases-related traits using UK Biobank (UKB) dataset for in-house usage

Postdoctoral Research

System Genomics lab
Baker Heart and Diabetes Institute

Melbourne, AU

Today - 2019

  • Under supervision of Prof Mike Inouye and Dr Shu Mei Teo (Senior Research fellow)
  • Leading integrative omics projects using a longitudinal cohort (Childhood Asthma Study)
  • Examined the extent of genetics of gene expressions in neonatal innate and adaptive immunity using genomics and transcriptomics data (manuscript in review by co-authors)
  • Evaluated relationships between neonatal innate immune response and asthma related traits using genomics, transcriptomics, nasal 16S microbiota, and non-omics data (manuscript in review by co-authors)
  • Contributed to the carbon footprint of bioinformatics tools project led by Dr Jason Grealey

Research Assistant

iOmics Programme
Life Sciences Institute

Singapore, SG

2019 - 2011

  • Under supervison of Prof Yik-Ying Teo
  • Experienced in managing and analysing multidisplinary research projects in and presented to both local and overseas collaborators
  • Contributed and managed the development of iOmics (genomics, pharmacogenomics, HLA typing, transcriptomics, lipidomics, miRNAs, epigenomics - DNA methylation) and its extension, the Singapore Gut Microbiome Study
  • Designed the study and wrote research protocol of The Singapore Gut Microbiome Study, although PIs conceived the idea to carry out research on the study
  • Experienced in managing Logistics and Recruitment of participants for Singapore Integrative Omics Study (iOmics)
  • Re-developed an open access decision tree builder for cost-effective assessment to a current tool called Plant-A-Tree®, version 1 (http://www.gear4health.com/page/i/plant-a-tree) using VBA
  • Assisted PI in his milestone reports for grants and IRB

Internship

Computational biology lab
Genome Institute of Singapore

Singapore, SG

2010 - 2010

  • Under supervision of A/P Niranjan Nagarajan
  • Re-tooling a published research software – GiRaF: Influenza Reassortment Detection using C++ for in house usage
  • Gained independent problem-solving skills in data processing and data analysis during the re-tooling process with C++

Teaching Experience

Student mentor

Saw Swee Hock School of Public Health
National University of Singapore

Singapore, SG

2019 - 2011

  • Aided and supported students for their research projects
  • 2 graduate students (Wai-Sum Yap and Chee-Wei Yew)on whole genome sequencing analysis and population genetics analysis
  • 1 Master student (Melissa Butjor) on haplotype phasing for her downstream association with nutrients info analysis
  • 2 undergraduate students (Kah-Yan Hoi and Evelyn Lim) on R programming for their epidemiological association analysis

NUS-MIT Healthcare Analytics Datathon

Saw Swee Hock School of Public Health
National University of Singapore

Singapore, SG

2017

  • Student Lead for topic of “Identify potential clinical determinants in predicting outcome of patients who present to hospital with an Out-of-Hospital Cardiac Arrest” using MIMIC/EICU databases

Human Whole Genome Sequencing Data Analysis workshop

Biotechnology Research Institute
University Malaysia Sabah

Sabah, MY

2014

  • Teaching assistant for whole genome sequencing analysis

Statistic for life sciences module - ST 1232

Department of Statistic and Applied Probability
National University of Singapore

Singapore, SG

2014

  • Relief Teaching assistant during tutorial classes, when R programming is needed for statistical analysis

Service Experience

Recruiter

Saw Swee Hock School of Public Health
National University of Singapore

Singapore, SG

N/A

  • Served on hiring committee for Research Assistant/Associate and participated in selection and interviewing processes

Skills and Training

Computational Tools

N/A

N/A

N/A

  • Next-Gen sequencing analysis (GATK, BWA, samtools, Bowtie, BLAST, STAR, Picard, FastQC, cutadapt, TrimGalore, PennCNV, BirdSuite)
  • Omics wide association analysis (PLINK, BOLT-LMM)
  • Genomic Imputation and Phasing analysis (IMPUTE, minimac, Shapeit, Beagle, Eagle)
  • Variant Annotation (SnpEff, Polyphen, SIFT, ANNOVAR)
  • Gene expression and co-expression analysis (edgeR, WGCNA, DGCA)
  • Functional annotation of pathways (DAVID, GSEA, Gorrila, enrichment R package)
  • Evolutionary relationship analysis (Phylotree, MEGA, ADMIXTURE, PHYLIP)
  • Microbiome profiling (MetaPhlAn version 1)
  • Various R packages for statistical analysis

Programming languages

N/A

N/A

N/A

  • R, Python, Perl, C++, Bash, Java, MySQL, HTML, VBA, Slurm, PBS, STATA commands

Certified standard Mental Health First Aider

Accredited by Mental Health First Aid Australia

Melbourne, AU

2024 - 2021

Scientific Communications

Using evidence to empower decisions: Health Technology Assessment

Health Intervention and Technology Assessment Program, Trainee

Singapore, SG

2019

Mapping the genetic diversity in cosmopolitan Malays and indigenous populations.

American Society of Human Genetics 2017 Annual Meeting, Poster

Orlando, USA

2017

Singapore Integrative Omics Cohort: Establishing multiple omics baseline for three Southeast Asian ethnic groups

American Society of Human Genetics 2016 Annual Meeting, Poster

Vancouver, CA

2016

Mapping the genetic diversity of HLA haplotypes in the Japanese populations

Japan Human Genetic Society 60th Conference, Poster

Tokyo, JPN

2015

Mapping the genetic diversity of HLA haplotype in Asia populations

American Society of Human Genetics 2012 Annual Meeting, Poster

San Francisco, USA

2012

Publications

Mutual Exclusion of Methanobrevibacter Species in the Human Gut Microbiota Facilitates Directed Cultivation of a Candidatus Methanobrevibacter Intestini Representative

Microbiology Spectrum, Read it here

N/A

2022

  • Adrian Low,[…],Woei-Yuh Saw,[…], Yik Ying Teo, Niranjan Nagarajan, Henning Seedorf

Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians

BioRxiv, Read it here

N/A

2022

  • Jean-Sebastien Gounot*, Chia Minghao*, Denis Bertrand*, Woei-Yuh Saw,[…], Teo Yik-Ying, Henning Seedorf, Niranjan Nagarajan

The Carbon Footprint of Bioinformatics

Molecular Biology and Evolution, Read it here

N/A

2022

  • Jason Grealey*, Loïc Lannelongue*, Woei-Yuh Saw,[…], Michael Inouye

Paternal gene pool of Malays in Southeast Asia and its applications for the early expansion of Austronesians

American Journal of Human Biology, Read it here

N/A

2021

  • Jin Sun,[…],Woei-Yuh Saw,[…],Yik-Ying Teo,Hui Li

Genome-wide identification of cis DNA methylation quantitative trait loci in three Southeast Asian Populations

Human Molecular Genetics, Read it here

N/A

2021

  • Irfahan Kassam,[…], Woei-Yuh Saw,[…], Yik-Ying Teo, Marie Loh

Extended-Spectrum β-Lactamase-Producing and mcr-1-Positive Escherichia coli from the Gut Microbiota of Healthy Singaporeans

Applied and Environmental Microbiology, Read it here

N/A

2021

  • Yichen Ding, Woei-Yuh Saw,[…], Niranjan Nagarajan, Yik Ying Teo, Henning Seedorf

Shared Signature of Recent Positive Selection on the TSBP1-BTNL2-HLA-DRA Genes in Five Native Populations from North Borneo

Genome Biology and Evolution, Read it here

N/A

2020

  • Boon-Peng Hoh,[…] , Woei-Yuh Saw,[…], Yik-Ying Teo, Vijay Kumar Subbiah, Shuhua Xu

Emergence of tigecycline- and eravacycline-resistant Tet(X4)-producing Enterobacteriaceae in the gut microbiota of healthy Singaporeans

Journal of Antimicrobial Chemotherapy, Read it here

N/A

2020

  • Yichen Ding, Woei-Yuh Saw,[…], Niranjan Nagarajan, Yik Ying Teo, Henning Seedorf

Interethnic analyses of blood pressure loci in populations of East Asian and European descent

Nature Communications, Read it here

N/A

2018

  • Fumihiko Takeuchi, Masato Akiyama,[…],Woei-Yuh Saw,[…], Michiaki Kubo & Norihiro Kato

Dataset on gene expression in the elderly after Mindfulness Awareness Practice or Health Education Program

Data in Brief, Read it here

N/A

2018

  • Hwee-Woon Lim, Woei-Yuh Saw,[…], Ene-Choo Tan

Genetic relatedness of indigenous ethnic groups in northern Borneo to neighboring populations from Southeast Asia, as inferred from genome-wide SNP data

Annals of Human Genetics, Read it here

N/A

2018

  • Chee Wei Yew,[…],Woei Yuh Saw,[…],S. Vijay Kumar

Genome-wide association meta-analysis highlights light-induced signaling as a driver for refractive error

Nature Genetics, Read it here

N/A

2018

  • Milly S. Tedja, Robert Wojciechowski,[…],Woei-Yuh Saw,[…], Caroline C. W. Klaver

Phylogeography of Y-chromosome haplogroup O3a2b2-N6 reveals patrilineal traces of Austronesian populations on the eastern coastal regions of Asia

PLOS ONE, Read it here

N/A

2017

  • Lan-Hai Wei ,Shi Yan ,[…],Woei-Yuh Saw,[…],Hui Li

The fine-scale genetic structure and evolution of the Japanese population

PLOS ONE, Read it here

N/A

2017

  • Fumihiko Takeuchi ,[…],Woei-Yuh Saw,[…],Yik-Ying Teo ,Norihiro Kato

Establishing multiple omics baselines for three Southeast Asian populations in the Singapore Integrative Omics Study

Nature Communications, Read it here

N/A

2017

  • Woei-Yuh Saw,[…],Yik-Ying Teo

Lipidomic profiling of plasma in a healthy Singaporean population to identify ethnic specific differences in lipid levels and associations with disease risk factors

Clinical Mass Spectometry, Read it here

N/A

2017

  • Husna Begum,[…],Woei-Yuh Saw,[…],Markus R. Wenk

Characterising private and shared signatures of positive selection in 37 Asian populations

European Journal of Human Genetics, Read it here

N/A

2017

  • Xuanyao Liu, Dongsheng Lu,Woei-Yuh Saw,[…],Yik-Ying Teo

Dissecting the genetic structure and admixture of four geographical Malay populations

Scientific Reports, Read it here

N/A

2015

  • Lian Deng,[…],Woei-Yuh Saw,[…], Yik-Ying Teo,Shuhua Xu

Differential positive selection of malaria resistance genes in three indigenous populations of Peninsular Malaysia

Human Genetics, Read it here

N/A

2015

  • Xuanyao Liu,[…],Woei-Yuh Saw,[…], Yik-Ying Teo,Boon-Peng Hoh

Mapping the genetic diversity of HLA haplotypes in the Japanese populations

Scientific Reports, Read it here

N/A

2015

  • Woei-Yuh Saw,[…], Yik-Ying Teo & Norihiro Kato

Predicting HLA alleles from high-resolution SNP data in three Southeast Asian populations

Scientific Reports, Read it here

N/A

2014

  • Nisha Esakimuthu Pillai, Yukinori Okada,Woei-Yuh Saw,[…], Paul I. W. De Bakker, Yik-Ying Teo

Risk for ACPA-positive rheumatoid arthritis is driven by shared HLA amino acid polymorphisms in Asian and European populations

Human Molecular Genetics, Read it here

N/A

2014

  • Yukinori Okada, Kwangwoo Kim,[…],Woei-Yuh Saw,[…], Yik-Ying Teo, Paul I.W. de Bakker, Soumya Raychaudhuri

Evaluating the possibility of detecting evidence of positive selection across Asia with sparse genotype data from the HUGO Pan-Asian SNP Consortium

BMC Genomics, Read it here

N/A

2014

  • Xuanyao Liu,Woei-Yuh Saw,[…],Yik-Ying Teo

Evaluating the coverage and potential of imputing the exome microarray with next-generation imputation using the 1000 Genomes Project

PLOS ONE, Read it here

N/A

2014

  • Erwin Tantoso,[…],Woei-Yuh Saw,[…],Yik-Ying Teo

Insights into the genetic structure and diversity of 38 South Asian Indians from deep whole-genome sequencing

PLOS Genetics, Read it here

N/A

2014

  • Lai-Ping Wong ,Jason Kuan-Han Lai ,Woei-Yuh Saw,[…],Yik-Ying Teo

The HLA-DRβ1 amino acid positions 11-13-26 explain the majority of SLE-MHC associations

Nature Communications, Read it here

N/A

2014

  • Kwangwoo Kim,[…],Woei-Yuh Saw, Yik-Ying Teo, Sang-Cheol Bae